Update for those who it might interest or help someday. I just about got it all put back together now. I ended up b/c of time and money just prep/painting the back half of the mower my self via an angle grinder with a wire wheel and some other air tools with some 3M abrasive pads. Not a perfect job by any means but it gets the job done. Heck, it will all be covered with grass soon enough.
Here's a run down, in no particular order, of what I had to replace/repair. It might help someone in this same situation to know what to expect.
1. All Hydraulic Hoses including high pressure and low pressure lines. I had a local hydraulic shop make the high pressure hoses based off the old ones and I also picked up all of the low pressure hose that I needed (3/8" and also 1/2")
2. I had to disassembled both Hydro pumps, which are Hydro-gear brand, b/c a lot of dirt and some water got in the openings since the hoses were burned off in the fire. I thought about trying to flush them but I also wanted to see what condition they were in. Now is the time to repair if necessary. Upon inspection I found that they were in over-all good condition. The main bearing for the shaft (number 6203) had a little play so I replaced it along with the thrust bearing. Neither were very expensive. Also replaced all the seals, obviously.
3. The drive motors (also hydro-gear brand) were also infiltrated with dirt and some water so I disassembled one of them and determined that the shaft had a pretty decent grove in it from the main shaft seal. Although it appeared to have not been leaking I just decided to purchase new drive motors and be done with it. Found them for a decent price from a place online called Pat's Small Engine Parts. They had the best price on factory original Hydro-gears and only $7.95 shipping.
4. Engine. I decided to swap it over to an air cooled motor rather than the original liquid cooled. After a lot of research and some advice from this forum (thanks mad mackie) I purchased a Kawasaki FX730v which is classified as a 26HP engine. I made sure it had the same size shaft, both length and diameter. Found the best deal from Small Engine Warehouse.
5. Wire harness. I obviously specified one that was for a Kawasaki air-cooled motor and also got the harness adapter to mate up the motor to the chassis harness.
6. All new safety switches, ignition module, pto switch, keyed start switch, and hour meter. The Wire harness came with a relay so now I got an extra one b/c I did not expect it to have.
7. New control cables for the choke and throttle. This model Kawasaki has two separate controls for the choke and throttle where as I think some Kholers have just one.
8. Seat. I got a factory scag seat. I'm not even going to tell you the price on this, it was absolutely disgusting.
9. Fuel Tanks. FYI they come with the barbs and gaskets/bushing but no fill caps.
10.The little Hydraulic tank on the back of the left fuel tank cost over $200 so I decided to make my own. I welded a 3/8 hose barb to the top for the return from the pumps and one of the old 90 deg. fittings from the old high pressure hydraulic line after cutting off the crimp. It worked really well. I'm still debating on how to install/fabricate the fill cap, any ideas or suggestions? (FYI, the fin on the back of the tank was just to attach the ground for welding)
11. Rod ends on the control handles had nylon inserts or races which melted so after determining the size and thread direction I ordered them from MSC. Also had to get the rod ends for the deck push bars.
12. Hydraulic oil cooler. On the liquid cooled model the bracket mounts to the side of the frame and is different then the one for the air cooled models. I modified the one that I had by cutting of the bottom vertical flange and welding on a horizontal flange that I made to fit existing holes in the chassis for mounting.
13. Exhaust manifold. I was not able to pin down the correct one to match my motor with my chassis so I had to modify my existing one off the liquid cooled motor. I had to cut the flanges off the muffler pipes and also the pipes themselves off the muffler. The pipes needed to be angled inward more while the flanges needed to be rotated slightly. Really wasn't too bad to do. It fits nicely now. Only question I have is if there is suppose to be a gasket between the flange and the cylinder head? Parts diagram does not indicate any.
There are abunch of other little parts that I ordered but really are just general maintenance parts like idlers, blade spindles, anti-scalp wheels, etc.
I still have to install the hydro pumps, drive motors, and hoses along with some other odds and ends, but the majority of the work, which was identifying and sourcing the correct parts, is done!
I hope that this will help someone in the future on their scag. Thanks again for the info and suggestions that were given.